BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524373.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,681,413 number of mapped reads = 1,560,720 (92.82%) number of supplementary alignments = 5,971 (0.36%) number of secondary alignments = 0 number of mapped bases = 91,873,319 bp number of sequenced bases = 91,847,120 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,061 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9855 >>>>>>> ACTG content number of A's = 22,179,997 bp (24.15%) number of C's = 18,006,890 bp (19.61%) number of T's = 29,992,282 bp (32.65%) number of G's = 21,656,248 bp (23.58%) number of N's = 11,703 bp (0.01%) GC percentage = 43.18% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 445,410 number of insertions = 6,587 mapped reads with insertion percentage = 0.42% number of deletions = 16,631 mapped reads with deletion percentage = 1.06% homopolymer indels = 44.02% >>>>>>> Coverage mean coverageData = 0.0297X std coverageData = 0.3063X There is a 2.66% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 7675348 0.03079369659825241 0.6726981601351844 chr2 243199373 7431549 0.03055743486641308 0.32859921025378513 chr3 198022430 6365789 0.0321468078136401 0.19457849392380397 chr4 191154276 6141933 0.03213076436752061 0.21792249396970562 chr5 180915260 5409262 0.02989942363070976 0.18875325937788864 chr6 171115067 3523796 0.02059313689775781 0.1681247715492523 chr7 159138663 5242946 0.032945771323967955 0.40359315235118265 chr8 146364022 4872384 0.03328949241364794 0.27597526601773353 chr9 141213431 3398765 0.02406828426964571 0.225281652983441 chr10 135534747 4591141 0.03387427284606213 0.2616285620738624 chr11 135006516 3817929 0.028279590593982887 0.23457917563429828 chr12 133851895 4314262 0.032231609421741844 0.20123038778093885 chr13 115169878 3025682 0.026271470045318622 0.17605142580643632 chr14 107349540 2540965 0.023670012931587783 0.17341077123227192 chr15 102531392 2869129 0.027982932290629585 0.18183156029690478 chr16 90354753 2858011 0.03163099787345996 0.20263053518181207 chr17 81195210 2496190 0.030743069695860138 0.21315909398153657 chr18 78077248 2533828 0.03245283440317978 0.38445451281656956 chr19 59128983 2599792 0.043968150103308894 0.4714822122582434 chr20 63025520 2643449 0.04194251788799204 0.2304649504711051 chr21 48129895 1261800 0.026216554181138354 0.19849254758124688 chr22 51304566 665466 0.012970892298358006 0.12287197797503308 chrMT 16571 16710 1.008388147969344 1.166664394728918 chrX 155270560 5297740 0.03411941065968977 0.22346043931439763 chrY 59373566 279453 0.004706690516112844 0.12854348107985333